I am going to run a game soon and the targets are going to speaking in codes [mostly lines from TV shows]. What skill[s] would cover this or is an Intuition check?

Sense Motive?

I use Logic+Intuition in situations where the characters have to solve or determine something.
If they have the appropriate knowledge skill, you might give them a bonus or add successes from a knowledge check as bonus dice.

Really? If the player chose a particular knowledge skill and they actually find a use for it, why not let them roll skill + attribute like they're supposed to? They're still using one of those two attributes after all. Knowledge skills are exactly what you need to solve and determine things I'd say.

Except for those challenges you let the players themselves have a crack at (no fun in being a dice-rolling machine!).

In this case, they are not trying to recognize the TV shows in question,
but their knowledge does help directly in breaking the code.
So it supplements the roll like good tools.

Also, my players choose their knowledge skills more for flavor than anything else;
everyone has logic and intuition, but not everyone has the knowledge skill in question,
so this gives everyone a chance to crack it, but a bonus to those with the skill.

I had thought about it, but they are going to be listning to 4+ hours of dailog, I might improvise some, but I don't want to go to crazy

If they are replacing words or sentences with words or sentences from TV-Shows (for example: "Switch to plan B" becomes "I love it when a plan comes together") and if they are using the same codes several times and if the people listening know a little bit about the circumstances, they can probably use a Decrypt program since it's just a form of substitution cypher.

I'd run it just like any language check. They are speaking a language with a specialization in TV Trivia(?). It would be like trying to figure out NetSpeak if you only knew english.